Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: RPKM to FPKM conversion
0
gravatar for kanwarjag
3.9 years ago by
kanwarjag • 1.0k
United States
kanwarjag • 1.0k wrote:

I have RNAseq data as RPKM values (tumor vs normal)  since data is paired end how could I convert to FPKM values. 

Thanks

 
rna-seq • 3.9k views
ADD COMMENT • link •
modified 3.9 years ago by michael.ante • 3.6k • written 3.9 years ago by kanwarjag • 1.0k
1

You may/should not convert RPKM to FPKM. You need to recalculate FPKM from BAM file. As suggested below, if you just divide by 2, they wont be true FPKM values as you do not knowif there are any read-pairs with only one-end mapped. And if there are many read pairs like that your FPKM value might not be true.

ADD REPLY • link modified 16 months ago by RamRS ♦ 25k • written 3.9 years ago by geek_y ♦ 10k

Thanks for the explanation

ADD REPLY • link modified 16 months ago by RamRS ♦ 25k • written 3.9 years ago by kanwarjag • 1.0k
2
gravatar for michael.ante
3.9 years ago by
michael.ante • 3.6k
Austria/Vienna
michael.ante • 3.6k wrote:

In case of single end data, RPKM=FPKM (Reads per kilobase per million reads and Fragments per kilobase per million reads).

In case of paired end data, you have for every read-pair one fragment. Thus, divide the RPKM by two.
ADD COMMENT • link modified 16 months ago by RamRS ♦ 25k • written 3.9 years ago by michael.ante • 3.6k

very naive clarification should it be tumor RPKM/2 - normal RPKM/2

or it should be tumor RPKM-normal RPKM = X/2

ADD REPLY • link modified 16 months ago by RamRS ♦ 25k • written 3.9 years ago by kanwarjag • 1.0k

If you are looking at the ratios/fold-changes, it doesn't matter. The factor 2 is cancelled:

4:1 == 2:0.5
ADD REPLY • link modified 16 months ago by RamRS ♦ 25k • written 3.9 years ago by michael.ante • 3.6k

got it 

ADD REPLY • link modified 3.9 years ago • written 3.9 years ago by kanwarjag • 1.0k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1878 users visited in the last hour